Examples with Extent org.vcell.util.Extent used on opensource projects

Example 86 with Extent

use of org.vcell.util.Extent in project vcell by virtualcell.

the class XmlHelper method imageToXML.

static String imageToXML(VCImage vcImage, boolean printKeys) throws XmlParseException {
    String xmlString = null;
    if (vcImage == null) {
        throw new XmlParseException("Invalid input for VCImage: " + vcImage);
    }
    Xmlproducer xmlProducer = new Xmlproducer(printKeys);
    Extent extent = vcImage.getExtent();
    Element container = new Element(IMAGE_CONTAINER);
    Element imageElement = xmlProducer.getXML(vcImage);
    Element extentElement = xmlProducer.getXML(extent);
    container.addContent(imageElement);
    container.addContent(extentElement);
    container = XmlUtil.setDefaultNamespace(container, Namespace.getNamespace(XMLTags.VCML_NS));
    xmlString = XmlUtil.xmlToString(container);
    return xmlString;
}

Example 87 with Extent

use of org.vcell.util.Extent in project vcell by virtualcell.

the class FunctionRangeGenerator method main.

public static void main(String[] args) {
    try {
        Expression exp = new Expression("a+log(b)+c");
        VarStatistics[] varStats = new VarStatistics[3];
        varStats[0] = new VarStatistics("a", new double[] { 1.0, 2.0, 3.0 }, new double[] { 1.0, 2.0, 3.0 });
        varStats[1] = new VarStatistics("b", new double[] { 1.0, 2.0, 3.0 }, new double[] { 1.0, 2.0, 3.0 });
        varStats[2] = new VarStatistics("c", new double[] { 1.0, 2.0, 3.0 }, new double[] { 1.0, 2.0, 3.0 });
        double[] times = new double[] { 0.0, 1.0, 2.0 };
        Extent extent = new Extent(5, 5, 5);
        Origin origin = new Origin(0, 0, 0);
        // int numSamplesPerDim = 10;
        byte[] pixels = new byte[3 * 3 * 3];
        BitSet indomain = new BitSet(pixels.length);
        for (int i = 0; i < pixels.length; i++) {
            indomain.set(i);
        }
        VCImageUncompressed vcImage = new VCImageUncompressed(null, pixels, extent, 3, 3, 3);
        RegionImage regionImage = new RegionImage(vcImage, 3, extent, origin, RegionImage.NO_SMOOTHING);
        CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, new ISize(regionImage.getNumX(), regionImage.getNumY(), regionImage.getNumZ()), regionImage, true);
        FunctionStatistics results = FunctionRangeGenerator.getFunctionStatistics(exp, varStats, times, mesh, indomain, VariableType.VOLUME);
        System.out.println(results.getDefaultDatasetRange().toString());
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 88 with Extent

use of org.vcell.util.Extent in project vcell by virtualcell.

the class DisplayTimeSeries method displayImageTimeSeries.

public static void displayImageTimeSeries(final ImageTimeSeries<Image> imageTimeSeries, String title, WindowListener windowListener) throws ImageException, IOException {
    ISize size = imageTimeSeries.getISize();
    int dimension = (size.getZ() > 0) ? (3) : (2);
    Extent extent = imageTimeSeries.getExtent();
    Origin origin = imageTimeSeries.getAllImages()[0].getOrigin();
    // don't care ... no surfaces
    double filterCutoffFrequency = 0.5;
    VCImage vcImage = new VCImageUncompressed(null, new byte[size.getXYZ()], extent, size.getX(), size.getY(), size.getZ());
    RegionImage regionImage = new RegionImage(vcImage, dimension, extent, origin, filterCutoffFrequency);
    final CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, size, regionImage);
    final DataIdentifier dataIdentifier = new DataIdentifier("var", VariableType.VOLUME, new Domain("domain"), false, "var");
    final DataSetController dataSetController = new DataSetController() {

        @Override
        public ExportEvent makeRemoteFile(OutputContext outputContext, ExportSpecs exportSpecs) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public TimeSeriesJobResults getTimeSeriesValues(OutputContext outputContext, VCDataIdentifier vcdataID, TimeSeriesJobSpec timeSeriesJobSpec) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public SimDataBlock getSimDataBlock(OutputContext outputContext, VCDataIdentifier vcdataID, String varName, double time) throws RemoteProxyException, DataAccessException {
            double timePoint = time;
            double[] timePoints = getDataSetTimes(vcdataID);
            int index = -1;
            for (int i = 0; i < timePoints.length; i++) {
                if (timePoint == timePoints[i]) {
                    index = i;
                    break;
                }
            }
            double[] data = imageTimeSeries.getAllImages()[index].getDoublePixels();
            PDEDataInfo pdeDataInfo = new PDEDataInfo(null, null, varName, time, 0);
            VariableType varType = VariableType.VOLUME;
            return new SimDataBlock(pdeDataInfo, data, varType);
        }

        @Override
        public boolean getParticleDataExists(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            return false;
        }

        @Override
        public ParticleDataBlock getParticleDataBlock(VCDataIdentifier vcdataID, double time) throws DataAccessException, RemoteProxyException {
            return null;
        }

        @Override
        public ODESimData getODEData(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            return null;
        }

        @Override
        public CartesianMesh getMesh(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            return mesh;
        }

        @Override
        public PlotData getLineScan(OutputContext outputContext, VCDataIdentifier vcdataID, String variable, double time, SpatialSelection spatialSelection) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public AnnotatedFunction[] getFunctions(OutputContext outputContext, VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            return new AnnotatedFunction[0];
        }

        @Override
        public double[] getDataSetTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            return imageTimeSeries.getImageTimeStamps();
        }

        @Override
        public DataSetTimeSeries getDataSetTimeSeries(VCDataIdentifier vcdataID, String[] variableNames) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public DataSetMetadata getDataSetMetadata(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public DataIdentifier[] getDataIdentifiers(OutputContext outputContext, VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            return new DataIdentifier[] { dataIdentifier };
        }

        @Override
        public FieldDataFileOperationResults fieldDataFileOperation(FieldDataFileOperationSpec fieldDataFileOperationSpec) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public DataOperationResults doDataOperation(DataOperation dataOperation) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public VtuFileContainer getEmptyVtuMeshFiles(VCDataIdentifier vcdataID, int timeIndex) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public double[] getVtuTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public double[] getVtuMeshData(OutputContext outputContext, VCDataIdentifier vcdataID, VtuVarInfo var, double time) throws RemoteProxyException, DataAccessException {
            // TODO Auto-generated method stub
            return null;
        }

        @Override
        public VtuVarInfo[] getVtuVarInfos(OutputContext outputContext, VCDataIdentifier vcDataIdentifier) throws DataAccessException, RemoteProxyException {
            // TODO Auto-generated method stub
            return null;
        }

        @Override
        public NFSimMolecularConfigurations getNFSimMolecularConfigurations(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            // TODO Auto-generated method stub
            return null;
        }
    };
    DataSetControllerProvider dataSetControllerProvider = new DataSetControllerProvider() {

        @Override
        public DataSetController getDataSetController() throws DataAccessException {
            return dataSetController;
        }
    };
    VCDataManager vcDataManager = new VCDataManager(dataSetControllerProvider);
    OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
    VCDataIdentifier vcDataIdentifier = new VCDataIdentifier() {

        public User getOwner() {
            return new User("nouser", null);
        }

        public KeyValue getDataKey() {
            return null;
        }

        public String getID() {
            return "mydata";
        }
    };
    PDEDataManager pdeDataManager = new PDEDataManager(outputContext, vcDataManager, vcDataIdentifier);
    ClientPDEDataContext myPdeDataContext = new ClientPDEDataContext(pdeDataManager);
    PDEDataViewer pdeDataViewer = new PDEDataViewer();
    JFrame jframe = new JFrame();
    jframe.setTitle(title);
    jframe.getContentPane().add(pdeDataViewer);
    jframe.setSize(1000, 600);
    jframe.setVisible(true);
    if (windowListener != null) {
        jframe.addWindowListener(windowListener);
    }
    pdeDataViewer.setPdeDataContext(myPdeDataContext);
}

Example 89 with Extent

use of org.vcell.util.Extent in project vcell by virtualcell.

the class FitBleachSpotOp method main.

public static void main(String[] args) {
    try {
        int numX = 100;
        int numY = 100;
        double center_i = 52.44;
        double center_j = 51.39;
        double K = 30;
        double high = 0.9;
        double sigma2 = 4;
        float[] pixels = new float[numX * numY];
        Origin origin = new Origin(0, 0, 0);
        Extent extent = new Extent(1, 1, 1);
        FloatImage image = new FloatImage(pixels, origin, extent, numX, numY, 1);
        int index = 0;
        for (int j = 0; j < numY; j++) {
            for (int i = 0; i < numX; i++) {
                double radius = ((i - center_i) * (i - center_i) + (j - center_j) * (j - center_j));
                pixels[index++] = (float) (high - FastMath.exp(-K * FastMath.exp(-radius / sigma2)));
            }
        }
        double init_center_i = 50;
        double init_center_j = 50;
        double init_sigma2 = 2;
        GaussianFitResults fitResults = fitToGaussian(init_center_i, init_center_j, init_sigma2, image);
        System.out.println(fitResults);
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 90 with Extent

use of org.vcell.util.Extent in project vcell by virtualcell.

the class FitBleachSpotOp method fit.

public FitBleachSpotOpResults fit(NormalizedSampleFunction bleachROI, FloatImage normImage) {
    // 
    // find initial guess by centroid from bleach ROI and total area of bleach ROI (assuming a circle of radius R)
    // 
    ISize size = bleachROI.getISize();
    if (size.getZ() > 1) {
        throw new RuntimeException("expecting 2D bleach region ROI");
    }
    short[] pixels = bleachROI.toROI(1e-5).getBinaryPixelsXYZ(1);
    long numPixelsInROI = 0;
    Extent extent = bleachROI.getExtent();
    double totalX_um = 0.0;
    double totalY_um = 0.0;
    double total_I = 0.0;
    double total_J = 0.0;
    int pixelIndex = 0;
    for (int i = 0; i < size.getX(); i++) {
        double x = extent.getX() * (i + 0.5) / (size.getX() - 1);
        for (int j = 0; j < size.getY(); j++) {
            if (pixels[pixelIndex] != 0) {
                double y = extent.getY() * (j + 0.5) / (size.getY() - 1);
                totalX_um += x;
                totalY_um += y;
                total_I += i;
                total_J += j;
                numPixelsInROI++;
            }
            pixelIndex++;
        }
    }
    Origin origin = bleachROI.getOrigin();
    double roiCenterX_um = origin.getX() + totalX_um / numPixelsInROI;
    double roiCenterY_um = origin.getY() + totalY_um / numPixelsInROI;
    double roiCenterI_pixelscale = total_I / numPixelsInROI;
    double roiCenterJ_pixelscale = total_J / numPixelsInROI;
    // Area = PI * R^2
    // R = sqrt(Area/PI)
    double roiBleachSpotArea_um2 = (extent.getX() * extent.getY() * numPixelsInROI) / (size.getX() * size.getY());
    double roiBleachRadius_um = Math.sqrt(roiBleachSpotArea_um2 / Math.PI);
    double roiBleachRadius_pixelscale = Math.sqrt(numPixelsInROI / Math.PI);
    FitBleachSpotOpResults results = new FitBleachSpotOpResults();
    results.bleachRadius_ROI = roiBleachRadius_um;
    results.centerX_ROI = roiCenterX_um;
    results.centerY_ROI = roiCenterY_um;
    GaussianFitResults gfresults = fitToGaussian(roiCenterI_pixelscale, roiCenterJ_pixelscale, roiBleachRadius_pixelscale * roiBleachRadius_pixelscale, normImage);
    results.bleachFactorK_GaussianFit = gfresults.K;
    results.bleachRadius_GaussianFit = Math.sqrt(gfresults.radius2);
    results.centerX_GaussianFit = origin.getX() + extent.getX() * (gfresults.centerI + 0.5) / size.getX();
    results.centerY_GaussianFit = origin.getY() + extent.getY() * (gfresults.centerJ + 0.5) / size.getY();
    return results;
}